Arabidopsis resource

Janine Sieja Hagerman jsh at ncgr.org
Wed Sep 29 12:44:21 EST 1999


UNDERSTANDING OF PLANT GENETICS BOOSTED
BY $5.3 MILLION NSF GRANT TO CARNEGIE INSTITUTION, NCGR 

STANFORD, Calif., and SANTA FE, N.M., Sept. 29 - By the end of next year,
scientists will know the entire genetic makeup of the Arabidopsis thaliana
plant, a mustard that is closely related to many food plants and used as a
model for all aspects of plant biology. Availability of so much data about
this plant-the first to be completely sequenced-is a significant step
toward understanding the biology of all plants and improving agriculturally
important crops such as corn, soybeans and rice. To make best use of these
data, the National Science Foundation has awarded a five-year, $5.3 million
grant to The Arabidopsis Information Resource (TAIR) project, a joint
venture of the Department of Plant Biology at the Carnegie Institution of
Washington in Stanford and the National Center for Genome Resources (NCGR)
in Santa Fe.

The NSF grant will support a new, publicly accessible database called TAIR,
which will contain all the information about the Arabidopsis genome project
and experimental data from literature to facilitate the analysis and
interpretation of the plant's genetic makeup. There is a direct link
between most, if not all, genes of the model plant and those of 250,000
other plant species, including commercially important ones. Arabidopsis,
however, is easier to study because it has a highly compact genome, with
about a third the amount of DNA as rice. TAIR will allow researchers to
compare the DNA sequences of other plants to those whose functions are
known in Arabidopsis to determine what role the genes in the other plants
may play. This, in turn, could hasten understanding of how to use plant
genetics to increase productivity, bolster resistance to disease and
optimize other desirable traits in the hundred or so commercially important
plant species. 

"We will be developing a comprehensive database of Arabidopsis data with
broad applications," said Chris Somerville, Ph.D., Director of Plant
Biology at Carnegie. "Because the value of Arabidopsis is its utility in
understanding other plants, our goal is to build a structure that permits
us to link information about Arabidopsis to all other plants, and vice
versa." 

TAIR will contain information about the Arabidopsis research community
(people, labs, companies and databases); DNA sequence and map data; allele,
phenotype, and stock data; gene, protein, and transcript data; experimental
data from the literature; as well as images and references. "With the
explosion of genomic data and the diversity of data types and methods,
biologists are in need of new ways of obtaining and analyzing 
data. TAIR will address this critical need by providing integrated and
value-added data in an industry-standard database environment," said Sue
Rhee, Ph.D., TAIR Director.


"TAIR gives us the opportunity to tackle a broad range of biological
challenges and data types," said Bruno W.S. Sobral, Ph.D., NCGR's Vice
President of Scientific Programs. "We will be creating our vision of the
genomic database of the future."

The user-friendly resource, which will be available at a Web site hosted by
NCGR, will feature an intuitive, object-oriented program that will use a
common vocabulary, have visualization tools and allow information retrieval
queried from any perspective. 

"TAIR will benefit from cross-pollination with other informatics programs
at NCGR, particularly comparative genomics, gene expression and metabolic
pathways," said Allan Dickerman, Ph.D., NCGR's TAIR coordinator.

The new database will replace the current Arabidopsis database (AtDB)
gradually and incrementally, with the release of the preliminary version of
the new database on Jan. 15, 2000, which will contain all data from AtDB. A
first version of TAIR, with new data and displays, will be released Sept.
1, 2000.

"NSF is committed to delivering a comprehensive information resource to the
international Arabidopsis research community," said Paul Gilna, Ph.D.,
Program Director of NSF's Biological Database and Informatics Program.  "We
believe that the size and duration of this award will allow for the
development of an increased ability to respond quickly to user community
needs.  We look forward to working together with the Carnegie Institution,
NCGR and the plant research community in developing a showcase example for
knowledge management in biology."


About the Carnegie Institution

The Carnegie Institution of Washington (www.ciw.edu), a private, nonprofit
organization, engages in basic research and advanced education in biology,
astronomy and the earth sciences. There are five research departments in
the U.S.: Terrestrial Magnetism, Plant Biology, Observatories, Embryology
and Geophysical Laboratory. The Department of Plant Biology, on the campus
of Stanford University, engages in basic research in modern plant science.
A long-term goal at the department is to integrate studies at the various
levels of biological organization, from the biochemical and molecular
experimentation to broad-ranging ecological research. Its philosophy of
training young scientists amplifies the potential of such integrative work.

About NCGR

The National Center for Genome Resources (www.ncgr.org) is dedicated to
enhancing the understanding of life through the research, development and
application of knowledge systems that support biological discovery. NCGR, a
nonprofit organization specializing in bioinformatics, merges biology and
computer science to help comprehend biological data, leading to
applications in agriculture, medicine and environmental science.



* * *
Janine Sieja Hagerman
Director of Public Affairs
National Center for Genome Resources
2960 Rodeo Park Drive, Second Floor
Santa Fe, NM 87505
505/995-4459, 4439 (fax)  




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